And the sample they sent is a fragment of Xenomorph DNA. It was their plan B in case the LV-223 facility WMD wouldn't work. So they sent a piece of genome of their most successful(according to EU successful enough to rebel against them and win) bioweapon and let our stupidity do the rest. Also, Sil and her ilk look an awful lot like a perfect mix of human and xenomorph, in appearance, mindset and abilities. The fact they can be tame and reasonable when treated like people and not like lab rats was not a problem for the Engineers, they know humanity all too well...

Sil and Patrick are not the same type of creature.

It would explain certain inconsistencies. why Sil took much longer to develop from fertilized egg to baby than seems normal for her species (she was presumably implanted in a human surrogate mother, and her species doesn't have whatever mechanisms allowed Patrick's offspring to just suck 7-9 pounds of material out of their hosts in minutes, so her early growth was dramatically slowed down). They are related but distinct species (or subspecies - they're obviously interfertile). This theory is also appealing because it removes the third movie's implication that any offspring Sil had would probably have been sickly and sterile so she could never have been a serious threat to humanity. And it would provide a handy excuse for any fanfic writers who might want to throw out some of the things we learned about the creatures in the second and third movie.

Since they seem to be artificial constructs to begin with, this makes a fair bit of sense.

Also, Patrick was infected by alien DNA leftover on Mars, which was implied to have wiped out a much earlier Martian civilization. So the alien DNA would have had Martian DNA mixed in with it, turning Patrick not into a straight human/alien hybrid, but a human/Martian/alien hybrid. Could also explain why the infected female astronaut didn't become Sil II (or III, depending on how you like to count.)

It could be possible the alien DNA that infected Patrick is a flawed mutation in itself. Whether by any other dna or just by it's own species. The team in the first movie kills the pure alien creature before much could be learned about it. But it seems strange that what they found on Mars would impregnate a human female and inject it's own dna into a human male. Perhaps it even knew it was a genetic failure to it's own kind, and was hoping to preserve it's line any way it could? And when Patrick came to Earth he brought those mutations with him?

The major problem in this line of thinking is that each step in this chain is itself some matter of hybrid. (if Patrick can really be called that?) Each with questions the movies never bother fully explaining to us. I think it's entirely possible Patrick's infector could have been a hybrid itself, a genetic mutation and/or a subspecies to the pure DNA that was sent. And even if a scifi setting, any of those things could totally cause genetic problems to his mating with humans or Eve.

The aliens are a seed/specialized unit of a superorganism.

The aliens are fast-maturing, fast-breeding creatures which seem to operate largely on hard-wired instinct, which isn't a life strategy that one would typically associate with selection for high intelligence. It would make sense, however, if they're specialized autonomous units designed to serve the purposes some larger superorganism, something like the Tyrannids or Zerg.

Well, according to Fitch they did first give us an infinite-energy methane formula, but when they gave their "friendly instructions" about how to construct a hybrid, they really didn't send their intentions.

Going off this, the reason the aliens are so crazy it not because of the alien DNA, but because of the Human DNA. Maybe the combination of both is what drives their aggressiveness and need to mate Up to Eleven and pure aliens are actually a peaceful, benign race. Of course, for this theory to work you have ignore what the scientists said about Mars in the second film, but given that: A) He was crazy and B) The movie was crap, we can just ignore it.

On the other hand, the "pure" example of alien DNA grew at a hyperfast rate, devouring every living thing it could reach. This may just be the way it normally spawns, including its fantastic metabolism, and it slows down once it's glutted itself. All the same, this is still dangerous for anything in its way, suggesting the species will actively hunt when it needs to.

Alternatively, the "infinite-energy methane equation" could have just been a ruse to "convince humanity they're dealing with a friendly intelligence" (Fitch says almost exactly this in the film) so that humans would unquestioningly perform the follow-up DNA experiment without pausing to consider the ramifications. Basically, these aliens are assholes.

The aliens were curious as to what we would do, to see if we really were a threat.

The aliens wanted to see how we'd react to the organism they sent along with the methane formula. They may have reasoned that their first gift would make us curious to try out the second, so we would naturally try to create and raise Sil and her kind. What would happen after that was the critical thing. Remember, one of the scientists speculates if the aliens consider humanity an "intergalactic weed" to be dealt with, and if Sil is meant to confront us. How we deal with her, whether we fight her, tame her, or fall to her, will reveal to them what we're capable of as a sentient species (and possibly how to be further considered.)

It's possible Sil's original species is not the same one that sent the message to Earth. The "pure" alien species grew abnormally fast, nearly killing the scientists next to it; it may be some predatory creature on the aliens' home world. There may have been more than one reason for sending its DNA here:

The aliens simply want to see what we do with it.

On their planet, "super-plants" have run wild, and the aliens are watching how we deal with one, hoping for a solution to a real problem on their home world.

Sil's home world is dying, and this is how the species colonize new worlds. The methane formula may be for their own later use, like sending supplies in advance of landing.

Sil and her kind are a test; if earthlings can confront her and survive, we've proven ourselves capable of overcoming threats.

Sil is still a test, but defeating her proves how dangerous we are.

Under this scenario, the Mars colony could be from some piece of space debris, the equivalent of a rat washing up on a deserted island, not really intentional. The alien species may have just been keeping an eye on our solar system because it looked interesting.

The aliens grow using the same method as plants.

As You Know plants absorb CO2 from the air and release oxygen. They use the retained carbon to grow and thus they acquire most of their mass from the air itself rather than absorbing it through the roots, as one might expect. The aliens may gain mass and regenerate with a similar process, just sucking carbon right out of the air as they grow. This also explains any other conservation of mass problem with aliens in sci-fi.

Hmm, Sil does have a rather distinctive green color to her alien skin. . .

The hot chick who boinked the guy to death in the men's room in Species 3 was the daughter of the 2nd woman in Patrick's threesome in Species 2

Look at them and tell me they aren't related.

Obviously Patrick is the father: there was no where else she could have come from. Sil's only child was a boy and both were killed. The second egg was Eve and the third went on to become the chick in Species 4. As for the women in the threesome, remember they were sisters, it could be either one.

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